From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) by finch.gentoo.org (Postfix) with ESMTP id 6176E58973 for ; Wed, 10 Feb 2016 13:31:21 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id DB6D821C032; Wed, 10 Feb 2016 13:31:17 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 6803921C032 for ; Wed, 10 Feb 2016 13:31:15 +0000 (UTC) Received: from oystercatcher.gentoo.org (unknown [IPv6:2a01:4f8:202:4333:225:90ff:fed9:fc84]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id B661B340A7F for ; Wed, 10 Feb 2016 13:31:14 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id B66A88E9 for ; Wed, 10 Feb 2016 13:31:11 +0000 (UTC) From: "Martin Mokrejs" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Martin Mokrejs" Message-ID: <1455110919.1a4dc5be8fd24487de1306cf68af5a7d507edb01.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/SnpEff/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/SnpEff/SnpEff-4.1e.ebuild sci-biology/SnpEff/metadata.xml X-VCS-Directories: sci-biology/SnpEff/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: 1a4dc5be8fd24487de1306cf68af5a7d507edb01 X-VCS-Branch: master Date: Wed, 10 Feb 2016 13:31:11 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: 72a9f7b9-a837-4748-b579-ec4795ad7007 X-Archives-Hash: aa67e92f77207798341a1f5c1e3e7526 commit: 1a4dc5be8fd24487de1306cf68af5a7d507edb01 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Wed Feb 10 13:28:39 2016 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Wed Feb 10 13:28:39 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=1a4dc5be sci-biology/SnpEff: version bump Package-Manager: portage-2.2.26 sci-biology/SnpEff/SnpEff-4.1e.ebuild | 56 +++++++++++++++++++++++++++++++++++ sci-biology/SnpEff/metadata.xml | 9 ++++++ 2 files changed, 65 insertions(+) diff --git a/sci-biology/SnpEff/SnpEff-4.1e.ebuild b/sci-biology/SnpEff/SnpEff-4.1e.ebuild new file mode 100644 index 0000000..5e9434a --- /dev/null +++ b/sci-biology/SnpEff/SnpEff-4.1e.ebuild @@ -0,0 +1,56 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit java-pkg-2 java-ant-2 + +[ "$PV" == "9999" ] && inherit git-2 + +DESCRIPTION="Annotate SNP changes and predict their effect" +HOMEPAGE="http://snpeff.sourceforge.net" + +if [ "$PV" == "9999" ]; then + EGIT_REPO_URI="https://github.com/pcingola/SnpEff.git" + #EGIT_BRANCH="v4.1B" + KEYWORDS="" +else + SRC_URI="http://sourceforge.net/projects/snpeff/files/snpEff_v4_1e_core.zip + http://snpeff.sourceforge.net/SnpSift.html -> ${P}.html" + KEYWORDS="~amd64" + S="${WORKDIR}" +fi + +LICENSE="LGPL-3" +SLOT="0" +IUSE="" + +# https://github.com/pcingola/SnpEff/blob/master/README_release.txt +DEPEND=">=virtual/jre-1.7:* + dev-java/maven-bin:* + dev-java/antlr:*" +RDEPEND="${DEPEND} + >=virtual/jdk-1.7:*" + +#src_compile(){ +# mvn || die +#} + +src_install(){ + cd .. || die + mkdir -p "${D}"/usr/share + # but portage does not install the .* files and subdirs, grr! + unzip "${DISTDIR}"/snpEff_v4_1e_core.zip -d "${D}"/usr/share || die "failed to unzip ${DISTDIR}/snpEff_v4_1e_core.zip" + sed -e 's#$HOME/tools/picard/#/usr/share/picard/lib/#' -i "${D}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die + sed -e 's#$HOME/tools/gatk/#/usr/share/gatk/lib/#' -i "${D}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die + sed -e 's#$HOME/snpEff/#/usr/share/snpEff/#' -i "${D}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die + sed -e 's#$HOME/snpEff/snpEff.config#/usr/share/snpEff/snpEff.config#' -i "${D}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die +} + +# now fetch the version-specific databases from http://sourceforge.net/projects/snpeff/files/databases/v4_1/ +# it also automagically fetches them but into /tmp/ unlike $CWD +# +# java -Xmx4g path/to/snpEff/snpEff.jar -c path/to/snpEff/snpEff.config GRCh37.75 path/to/snps.vcf +# +# It is best to just unpack the tarball locally and not use portage at all. diff --git a/sci-biology/SnpEff/metadata.xml b/sci-biology/SnpEff/metadata.xml new file mode 100644 index 0000000..2bc8930 --- /dev/null +++ b/sci-biology/SnpEff/metadata.xml @@ -0,0 +1,9 @@ + + + + sci-biology + + mmokrejs@fold.natur.cuni.cz + Martin Mokrejs + +